version 1.1.3

.Rbuildignore

@@ -1,10 +1,10 @@
-^visual_test/$
+^visual_test/
 ^.*\.Rproj/$
-^\.Rproj\.user/$
+^\.Rproj\.user/
 ^\.travis\.yml$
 ^data-raw$
-^prepare_data$
-^packrat/$
+^prepare_data/
+^packrat/
 ^\.Rprofile$
 ^README.md$
 ^\.git/

R/zzz.R

@@ -1,8 +1,8 @@
 .onAttach <- function(libname, pkgname){
   packageStartupMessage(
-    "g3viz: visualizing gene/genome/gentics data for fun.
-    - Pfam (v33.1)
-    - UniProt (date: 2020/08/24)\n
-    Any questions, please send emails to <[email protected]> or post on GitHub <https://github.com/G3viz/g3viz/issues>."
+"g3viz: visualizing gene/genome/gentics data for fun.
+  - Pfam (v33.1)
+  - UniProt (date: 2020/08/24)\n
+Any questions, please send emails to <[email protected]> or post on GitHub <https://github.com/G3viz/g3viz/issues>."
     )
 }

prepare_data/generate_hgnc2pfam.R

@@ -88,5 +88,5 @@ hgnc2pfam.df <- hgnc2pfam.df[, c("symbol", "uniprot", "length",
                                  "start", "end", "hmm.acc", "hmm.name", "type")]
 
 # create Rdata, move this to "data" directory
-save(hgnc2pfam.df, file="hgnc2pfam.df.rda")
+save(hgnc2pfam.df, file="hgnc2pfam.df.rda", compress = "xz")
 

vignettes/introduction.Rmd

@@ -232,7 +232,7 @@ g3Lollipop(mutation.dat,
 [cBioPortal](http://www.cbioportal.org/) provides download for many cancer genomics data sets.
 `g3viz` has a convenient way to retrieve data directly from this portal.
 
-In this example, we first retrieve genetic mutation data of `TP53` gene for the [msk\_impact\_2017](https://www.ncbi.nlm.nih.gov/pubmed/28481359) study,
+In this example, we first retrieve genetic mutation data of `TP53` gene for the [msk\_impact\_2017](https://pubmed.ncbi.nlm.nih.gov/28481359/) study,
 and then visualize the data using the built-in `cbioportal` theme, to miminc cBioPortal's [mutation_mapper](https://www.cbioportal.org/mutation_mapper).
 
 <a name="cbioportal_theme"></a>